Spatially resolved T cell receptor diversity mapping uncovers variability of the cancer immune microenvironment

T cell receptor (TCR) binding properties have been related to a wide range of pathological conditions, including infections, autoimmunity and cancer. Characterising the TCR repertoire is of great biomedical interest but it has been challenging due to its high structural diversity.

In situ sequencing (ISS) is a suitable technique for spatial cell typing and linking gene patterns directly to specific histopathological features of large biopsy areas. We applied ISS through the commercial Xenium platform, with the addition of a custom panel specifically designed for TCR gene detection. Based on the IMGT database, we selected unique target sequences for TCR genes encoding the constant, variable and joining TCR chains. Additionally, we developed an analysis pipeline for the assignment of putative clonotypes based on simultaneous expression of alpha and beta variable TCR chains (TCRVβ/Vα pairs) at the single-cell level.

Our approach captured specific immune cell distributions in relation to the individual sample clonality, as well as regional dominance of certain TCRVβ/Vα pairs in surgical non-small cell lung cancer (NSCLC) specimens and matching lymph node samples. Furthermore, we were able to study the spatiotemporal evolution of TCR repertoire on longitudinal FFPE biopsies from patients with breast cancer, during neoadjuvant treatment.

This study highlights the implementation of target-based spatially resolved transcriptomics for the spatial characterisation of TCRVβ/Vα pairs at the single-cell level, without the need for prior sequencing. Our approach allows for spatial immune characterisation of diagnostic tissue samples with emphasis on T cell biology and accompanying T cell diversity.

This study was supported from Cancerfonden (CAN 2021/1726), Swedish Research Council (Dnr: 2019-01238), U-CAN and the Trond Mohn Foundation.